What does the scenario skip potion not give you?

[Fendred]

You know you could always just check the guide SE has up for it on the Mogstation which explains everything.
http://na.finalfantasyxiv.com/tales_...ure/#mainquest

Yes, that doesn't state whether the various minions and other quest-only items will be available for purchase or to acquire later. I used the job jump potion and it did not provide the AF 1 that a person normally gets as they progress to level 50. I was able to purchase that from the calamity salvage vendor, so no harm done. I have no such assurances for the scenario jump potion.

Your reward is skipping the story. Is that not enough?

It's not a reward. It's a purchase. You are buying completion of the main story and everything that entails. It does not say anywhere in its cost that the player forfeits unique quest only items as a result of the purchase.